ir (version 0.4.1)

ir_as_ir: Converts an object to class ir

Description

ir_as_ir converts an object to an object of class ir.

Usage

ir_as_ir(x, ...)
# S3 method for ir
ir_as_ir(x, ...)
# S3 method for data.frame
ir_as_ir(x, ...)
# S3 method for ir_flat
ir_as_ir(x, ...)
# S3 method for hyperSpec
ir_as_ir(x, ...)
# S3 method for Spectra
ir_as_ir(x, ...)

Value

An object of class ir with available metadata from original objects.

Arguments

x

An object.

...

Further arguments passed to individual methods.

• If x is a data frame, an object of class ir, an object of class hyperSpec (from package 'hyperSpec'), or an object of class Spectra (from package 'ChemoSpec'), these are ignored.

Examples

# conversion from an ir object
ir::ir_sample_data |>
  ir_as_ir()

# conversion from a data frame
x_ir <- ir::ir_sample_data

x_df <-
  x_ir |>
  ir_drop_spectra() |>
  dplyr::mutate(
    spectra = x_ir$spectra
  ) |>
  ir_as_ir()

# check that ir_as_ir preserves the input class
ir_sample_data |>
  structure(class = setdiff(class(ir_sample_data), "ir")) |>
  dplyr::group_by(sample_type) |>
  ir_as_ir()


# conversion from an ir_flat object
x_ir <-
  ir::ir_sample_data |>
  ir::ir_flatten() |>
  ir::ir_as_ir()

# conversion from a hyperSpec object from package hyperSpec
if(requireNamespace("hyperSpec")) {
  x_hyperSpec <- hyperSpec::laser
  x_ir <- ir_as_ir(x_hyperSpec)
}

# conversion from a Spectra object from class ChemoSpec
if(requireNamespace("ChemoSpec")) {

  ## sample data
  x <- ir_sample_data
  x_flat <- ir_flatten(x)

  ## creation of the object of class "Spectra" (the ChemoSpec package does
  ## not contain a sample Spectra object)
  n <- nrow(x)
  group_vector <- seq(from = 1, to = n, by = 1)
  color_vector <- rep("black", times = n)
  x_Spectra <- list() # dummy list
  x_Spectra$freq <- as.numeric(x_flat[,1, drop = TRUE]) # wavenumber vector
  x_Spectra$data <- as.matrix(t(x_flat[,-1])) # absorbance values as matrix
  x_Spectra$names <- as.character(seq_len(nrow(x))) # sample names
  x_Spectra$groups <- as.factor(group_vector) # grouping vector
  x_Spectra$colors <- color_vector # colors used for groups in plots
  x_Spectra$sym <- as.numeric(group_vector) # symbols used for groups in plots
  x_Spectra$alt.sym <- letters[as.numeric(group_vector)] # letters used for groups in plots
  x_Spectra$unit <- c("wavenumbers", "intensity") # unit of x and y axes
  x_Spectra$desc <- "NULL" # optional descriptions in plots
  attr(x_Spectra, "class") <- "Spectra"

  # conversion to ir
  x_ir <- ir_as_ir(x_Spectra)
}